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- PDB-2qqo: Crystal Structure of the a2b1b2 Domains from Human Neuropilin-2 -

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Basic information

Entry
Database: PDB / ID: 2qqo
TitleCrystal Structure of the a2b1b2 Domains from Human Neuropilin-2
ComponentsNeuropilin-2Neuropilin
KeywordsSIGNALING PROTEIN / VEGF receptor / semaphorin receptor / calcium-binding domain / Developmental protein / Differentiation / Glycoprotein / Membrane / Neurogenesis / Transmembrane / HORMONE
Function / homology
Function and homology information


vestibulocochlear nerve structural organization / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / trigeminal ganglion development / trigeminal nerve structural organization / sensory neuron axon guidance / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus ...vestibulocochlear nerve structural organization / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / trigeminal ganglion development / trigeminal nerve structural organization / sensory neuron axon guidance / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / branchiomotor neuron axon guidance / axon extension involved in axon guidance / NrCAM interactions / sympathetic neuron projection extension / Neurophilin interactions with VEGF and VEGFR / sympathetic ganglion development / neural crest cell migration involved in autonomic nervous system development / vascular endothelial growth factor receptor activity / nerve development / semaphorin receptor complex / outflow tract septum morphogenesis / semaphorin receptor activity / regulation of postsynapse organization / negative chemotaxis / cytokine binding / growth factor binding / semaphorin-plexin signaling pathway / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / cellular response to leukemia inhibitory factor / axon guidance / signaling receptor activity / heparin binding / postsynaptic membrane / angiogenesis / cell adhesion / axon / glutamatergic synapse / extracellular region / membrane / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Spermadhesin, CUB domain / Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MAM domain, meprin/A5/mu / MAM domain / Coagulation factors 5/8 type C domain (FA58C) signature 2. / MAM domain profile. / CUB domain ...Spermadhesin, CUB domain / Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MAM domain, meprin/A5/mu / MAM domain / Coagulation factors 5/8 type C domain (FA58C) signature 2. / MAM domain profile. / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Spermadhesin, CUB domain superfamily / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsAppleton, B.A. / Wiesmann, C.
CitationJournal: Embo J. / Year: 2007
Title: Structural studies of neuropilin/antibody complexes provide insights into semaphorin and VEGF binding
Authors: Appleton, B.A. / Wu, P. / Maloney, J. / Yin, J. / Liang, W.C. / Stawicki, S. / Mortara, K. / Bowman, K.K. / Elliott, J.M. / Desmarais, W. / Bazan, J.F. / Bagri, A. / Tessier-Lavigne, M. / ...Authors: Appleton, B.A. / Wu, P. / Maloney, J. / Yin, J. / Liang, W.C. / Stawicki, S. / Mortara, K. / Bowman, K.K. / Elliott, J.M. / Desmarais, W. / Bazan, J.F. / Bagri, A. / Tessier-Lavigne, M. / Koch, A.W. / Wu, Y. / Watts, R.J. / Wiesmann, C.
History
DepositionJul 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuropilin-2
B: Neuropilin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,44911
Polymers103,8752
Non-polymers5759
Water6,575365
1
A: Neuropilin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1624
Polymers51,9371
Non-polymers2243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neuropilin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2887
Polymers51,9371
Non-polymers3506
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.093, 192.909, 66.169
Angle α, β, γ (deg.)90.000, 90.080, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
33A
43B

NCS domain segments:

Refine code: 5

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPHISHISAA148 - 2687 - 127
211ASPASPHISHISBB148 - 2687 - 127
112GLNGLNARGARGAA276 - 428135 - 287
212GLNGLNARGARGBB276 - 428135 - 287
113VALVALGLYGLYAA429 - 509288 - 368
213VALVALGLYGLYBB429 - 509288 - 368
323ALAALAASPASPAA517 - 593376 - 452
423ALAALAASPASPBB517 - 593376 - 452

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Neuropilin-2 / Neuropilin / Vascular endothelial cell growth factor 165 receptor 2


Mass: 51937.301 Da / Num. of mol.: 2 / Fragment: CUB 2, F5/8 type C 1, and F5/8 type C 2 domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRP2, VEGF165R2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O60462
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.04 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes, 10% PEG 8000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 52659 / % possible obs: 94.5 % / Redundancy: 4.2 % / Rsym value: 0.056 / Χ2: 1.06 / Net I/σ(I): 14
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 4766 / Rsym value: 0.344 / Χ2: 0.904 / % possible all: 85.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QQJ (b1b2 domains), 2QQK (a2 domain)
Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 11.817 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.26 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2679 5.1 %RANDOM
Rwork0.185 ---
obs0.188 49667 94.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.764 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20.02 Å2
2--0.08 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6813 0 34 365 7212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227024
X-RAY DIFFRACTIONr_bond_other_d0.0010.024861
X-RAY DIFFRACTIONr_angle_refined_deg1.441.9489527
X-RAY DIFFRACTIONr_angle_other_deg0.8973.00311753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1495849
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.28523.547327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.393151150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6071550
X-RAY DIFFRACTIONr_chiral_restr0.0870.21013
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027767
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021452
X-RAY DIFFRACTIONr_nbd_refined0.1790.21002
X-RAY DIFFRACTIONr_nbd_other0.1950.24782
X-RAY DIFFRACTIONr_nbtor_refined0.1750.23089
X-RAY DIFFRACTIONr_nbtor_other0.0830.23696
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2285
X-RAY DIFFRACTIONr_metal_ion_refined0.1090.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2040.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.210
X-RAY DIFFRACTIONr_mcbond_it3.1082.54448
X-RAY DIFFRACTIONr_mcbond_other0.8612.51726
X-RAY DIFFRACTIONr_mcangle_it4.34556895
X-RAY DIFFRACTIONr_scbond_it3.3482.53074
X-RAY DIFFRACTIONr_scangle_it4.60552632
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1661MEDIUM POSITIONAL0.160.5
1868LOOSE POSITIONAL0.555
1661MEDIUM THERMAL0.812
1868LOOSE THERMAL1.8610
2902MEDIUM POSITIONAL0.110.5
21180LOOSE POSITIONAL0.485
2902MEDIUM THERMAL0.852
21180LOOSE THERMAL1.6710
3921MEDIUM POSITIONAL0.140.5
31231LOOSE POSITIONAL0.465
3921MEDIUM THERMAL0.932
31231LOOSE THERMAL1.8610
LS refinement shellResolution: 2.3→2.347 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.308 129 -
Rwork0.233 2603 -
all-2732 -
obs--85.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.8442-0.01512.35621.68730.30224.98060.05220.1499-0.1284-0.49410.1982-0.04740.08320.1381-0.25040.10320.0087-0.0042-0.1172-0.0236-0.13514.4915-20.8716-11.0295
21.98290.6730.50552.1607-0.01430.9649-0.03580.0421-0.0232-0.19770.1003-0.1905-0.21050.1437-0.0645-0.0485-0.030.0832-0.0449-0.0514-0.042420.5299-5.77689.4868
32.09961.3746-0.80132.8537-0.05850.58810.1505-0.2912-0.09790.2484-0.175-0.12890.0241-0.02920.0245-0.05450.0104-0.0292-0.01680.0403-0.0621-1.2724-27.364920.1482
42.10880.1821-1.79351.48450.2094.96380.17260.14360.2001-0.41870.1643-0.0335-0.1126-0.2071-0.33690.09170.0540.0319-0.11760.0257-0.1054-1.397623.404821.9243
51.740.4417-0.69582.1389-0.3321.2725-0.03450.1140.042-0.20460.09910.19850.319-0.1848-0.0646-0.0071-0.04-0.0922-0.0330.0199-0.0598-17.328.331742.5493
61.60170.30420.09382.23370.02260.88950.1583-0.24470.07890.0877-0.0358-0.0453-0.04940.166-0.1226-0.07320.00450.0305-0.0135-0.0494-0.03724.458330.207453.0129
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA148 - 2687 - 127
2X-RAY DIFFRACTION1AC11
3X-RAY DIFFRACTION2AA276 - 428135 - 287
4X-RAY DIFFRACTION3AA429 - 595288 - 454
5X-RAY DIFFRACTION4BB148 - 2687 - 127
6X-RAY DIFFRACTION4BD11
7X-RAY DIFFRACTION5BB276 - 428135 - 287
8X-RAY DIFFRACTION6BB429 - 593288 - 452

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